Updates to documentation
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Clair Blacketer
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***OMOP Common Data Model v5.3 Specifications***
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***OMOP Common Data Model v6.0 Specifications***
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<br>*Authors: Christian Reich, Patrick Ryan, Rimma Belenkaya, Karthik Natarajan, Clair Blacketer*
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<br>*3 January 2018*
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<br>*11 October 2018*
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Welcome to the Common Data Model wiki! This wiki houses all of the documentation for the latest version as well as changes added with each release. You can find a pdf added to each [release](https://github.com/OHDSI/CommonDataModel/releases) with a historical version of the wiki as it was at the time of the release. You can navigate the pages using the table of contents below or the links to the right.
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# Table of Contents
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**[License](wiki/License)**
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<br>
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<br>**[Background](wiki/Background)**
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<br> [The Role of the Common Data Model](wiki/The-Role-of-the-Common-Data-Model)
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<br> [Design Principles](wiki/Design-Principles)
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<br> [Data Model Conventions](wiki/Data-Model-Conventions)
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<br> [Frequently Asked Questions](wiki/Frequently-Asked-Questions)
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<br>
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<br>**[Glossary of Terms](wiki/Glossary-of-Terms)**
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<br>
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<br>**[Standardized Vocabularies](wiki/Standardized-Vocabularies)**
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<br>[CONCEPT](wiki/CONCEPT)
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<br>[VOCABULARY](wiki/VOCABULARY)
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<br>[DOMAIN](wiki/DOMAIN)
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<br>[CONCEPT_CLASS](wiki/CONCEPT_CLASS)
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<br>[CONCEPT_RELATIONSHIP](wiki/CONCEPT_RELATIONSHIP)
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<br>[RELATIONSHIP](wiki/RELATIONSHIP)
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<br>[CONCEPT_SYNONYM](wiki/CONCEPT_SYNONYM)
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<br>[CONCEPT_ANCESTOR](wiki/CONCEPT_ANCESTOR)
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<br>[SOURCE_TO_CONCEPT_MAP](wiki/SOURCE_TO_CONCEPT_MAP)
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<br>[DRUG_STRENGTH](wiki/DRUG_STRENGTH)
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<br>[COHORT_DEFINITION](wiki/COHORT_DEFINITION)
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<br>[ATTRIBUTE_DEFINITION](wiki/ATTRIBUTE_DEFINITION)
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<br>
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<br>**[Standardized Metadata](wiki/Standardized-Metadata)**
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<br>[CDM_SOURCE](wiki/CDM_SOURCE)
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<br>[METADATA](wiki/METADATA)
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<br>
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<br>**[Standardized Clinical Data Tables](Standardized-Clinical-Data-Tables)**
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<br>[PERSON](wiki/PERSON)
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<br>[OBSERVATION_PERIOD](wiki/OBSERVATION_PERIOD)
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<br>[SPECIMEN](wiki/SPECIMEN)
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<br>[DEATH](wiki/DEATH)
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<br>[VISIT_OCCURRENCE](wiki/VISIT_OCCURRENCE)
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<br>[VISIT_DETAIL](wiki/VISIT_DETAIL)
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<br>[PROCEDURE_OCCURRENCE](wiki/PROCEDURE_OCCURRENCE)
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<br>[DRUG_EXPOSURE](wiki/DRUG_EXPOSURE)
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<br>[DEVICE_EXPOSURE](wiki/DEVICE_EXPOSURE)
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<br>[CONDITION_OCCURRENCE](wiki/CONDITION_OCCURRENCE)
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<br>[MEASUREMENT](wiki/MEASUREMENT)
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<br>[NOTE](wiki/NOTE)
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<br>[NOTE_NLP](wiki/NOTE_NLP)
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<br>[OBSERVATION](wiki/OBSERVATION)
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<br>[FACT_RELATIONSHIP](wiki/FACT_RELATIONSHIP)
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<br>
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<br>**[Standardized Health System Data Tables](wiki/Standardized-Health-System-Data-Tables)**
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<br>[LOCATION](wiki/LOCATION)
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<br>[CARE_SITE](wiki/CARE_SITE)
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<br>[PROVIDER](wiki/PROVIDER)
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<br>
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<br>**[Standardized Health Economics Data Tables](wiki/Standardized-Health-Economics-Data-Tables)**
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<br>[PAYER_PLAN_PERIOD](wiki/PAYER_PLAN_PERIOD)
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<br>[COST](wiki/COST)
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<br>
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<br>**[Standardized Derived Elements](wiki/Standardized-Derived-Elements)**
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<br>[COHORT](wiki/COHORT)
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<br>[COHORT_ATTRIBUTE](wiki/COHORT_ATTRIBUTE)
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<br>[DRUG_ERA](wiki/DRUG_ERA)
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<br>[DOSE_ERA](wiki/DOSE_ERA)
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<br>[CONDITION_ERA](wiki/CONDITION_ERA)
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**[Home](https://github.com/OHDSI/CommonDataModel/wiki)**
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**[License](https://github.com/OHDSI/CommonDataModel/wiki/License)**
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**[Background](https://github.com/OHDSI/CommonDataModel/wiki/Background)**
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* [The Role of the Common Data Model](https://github.com/OHDSI/CommonDataModel/wiki/The-Role-of-the-Common-Data-Model)
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* [Design Principles](https://github.com/OHDSI/CommonDataModel/wiki/Design-Principles)
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* [Data Model Conventions](https://github.com/OHDSI/CommonDataModel/wiki/Data-Model-Conventions)
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* [Frequently Asked Questions](https://github.com/OHDSI/CommonDataModel/wiki/Frequently-Asked-Questions)
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**[Glossary of Terms](https://github.com/OHDSI/CommonDataModel/wiki/Glossary-of-Terms)**
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**[Standardized Vocabularies](https://github.com/OHDSI/CommonDataModel/wiki/Standardized-Vocabularies)**
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* [CONCEPT](https://github.com/OHDSI/CommonDataModel/wiki/CONCEPT)
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* [VOCABULARY](https://github.com/OHDSI/CommonDataModel/wiki/VOCABULARY)
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* [DOMAIN](https://github.com/OHDSI/CommonDataModel/wiki/DOMAIN)
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* [CONCEPT_CLASS](https://github.com/OHDSI/CommonDataModel/wiki/CONCEPT_CLASS)
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* [CONCEPT_RELATIONSHIP](https://github.com/OHDSI/CommonDataModel/wiki/CONCEPT_RELATIONSHIP)
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* [RELATIONSHIP](https://github.com/OHDSI/CommonDataModel/wiki/RELATIONSHIP)
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* [CONCEPT_SYNONYM](https://github.com/OHDSI/CommonDataModel/wiki/CONCEPT_SYNONYM)
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* [CONCEPT_ANCESTOR](https://github.com/OHDSI/CommonDataModel/wiki/CONCEPT_ANCESTOR)
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* [SOURCE_TO_CONCEPT_MAP](https://github.com/OHDSI/CommonDataModel/wiki/SOURCE_TO_CONCEPT_MAP)
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* [DRUG_STRENGTH](https://github.com/OHDSI/CommonDataModel/wiki/DRUG_STRENGTH)
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**[Standardized Metadata](https://github.com/OHDSI/CommonDataModel/wiki/Standardized-Metadata)**
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* [CDM_SOURCE](https://github.com/OHDSI/CommonDataModel/wiki/CDM_SOURCE)
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* [METADATA](https://github.com/OHDSI/CommonDataModel/wiki/METADATA)
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**[Standardized Clinical Data Tables](https://github.com/OHDSI/CommonDataModel/wiki/Standardized-Clinical-Data-Tables)**
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* [PERSON](https://github.com/OHDSI/CommonDataModel/wiki/PERSON)
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* [OBSERVATION_PERIOD](https://github.com/OHDSI/CommonDataModel/wiki/OBSERVATION_PERIOD)
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* [VISIT_OCCURRENCE](https://github.com/OHDSI/CommonDataModel/wiki/VISIT_OCCURRENCE)
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* [VISIT_DETAIL](https://github.com/OHDSI/CommonDataModel/wiki/VISIT_DETAIL)
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* [CONDITION_OCCURRENCE](https://github.com/OHDSI/CommonDataModel/wiki/CONDITION_OCCURRENCE)
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* [DEATH](https://github.com/OHDSI/CommonDataModel/wiki/DEATH)
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* [DRUG_EXPOSURE](https://github.com/OHDSI/CommonDataModel/wiki/DRUG_EXPOSURE)
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* [PROCEDURE_OCCURRENCE](https://github.com/OHDSI/CommonDataModel/wiki/PROCEDURE_OCCURRENCE)
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* [DEVICE_EXPOSURE](https://github.com/OHDSI/CommonDataModel/wiki/DEVICE_EXPOSURE)
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* [MEASUREMENT](https://github.com/OHDSI/CommonDataModel/wiki/MEASUREMENT)
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* [NOTE](https://github.com/OHDSI/CommonDataModel/wiki/NOTE)
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* [NOTE_NLP](https://github.com/OHDSI/CommonDataModel/wiki/NOTE_NLP)
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* [SURVEY_CONDUCT](https://github.com/OHDSI/CommonDataModel/wiki/SURVEY_CONDUCT)
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* [OBSERVATION](https://github.com/OHDSI/CommonDataModel/wiki/OBSERVATION)
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* [SPECIMEN](https://github.com/OHDSI/CommonDataModel/wiki/SPECIMEN)
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* [FACT_RELATIONSHIP](https://github.com/OHDSI/CommonDataModel/wiki/FACT_RELATIONSHIP)
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**[Standardized Health System Data Tables](https://github.com/OHDSI/CommonDataModel/wiki/Standardized-Health-System-Data-Tables)**
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* [LOCATION](https://github.com/OHDSI/CommonDataModel/wiki/LOCATION)
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* [LOCATION_HISTORY](https://github.com/OHDSI/CommonDataModel/wiki/LOCATION_HISTORY)
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* [CARE_SITE](https://github.com/OHDSI/CommonDataModel/wiki/CARE_SITE)
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* [PROVIDER](https://github.com/OHDSI/CommonDataModel/wiki/PROVIDER)
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**[Standardized Health Economics Data Tables](https://github.com/OHDSI/CommonDataModel/wiki/Standardized-Health-Economics-Data-Tables)**
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* [PAYER_PLAN_PERIOD](https://github.com/OHDSI/CommonDataModel/wiki/PAYER_PLAN_PERIOD)
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* [COST](https://github.com/OHDSI/CommonDataModel/wiki/COST)
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**[Standardized Derived Elements](https://github.com/OHDSI/CommonDataModel/wiki/Standardized-Derived-Elements)**
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* [DRUG_ERA](https://github.com/OHDSI/CommonDataModel/wiki/DRUG_ERA)
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* [DOSE_ERA](https://github.com/OHDSI/CommonDataModel/wiki/DOSE_ERA)
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* [CONDITION_ERA](https://github.com/OHDSI/CommonDataModel/wiki/CONDITION_ERA)
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**[Results Schema](https://github.com/OHDSI/CommonDataModel/wiki/Results-Schema)**
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* [COHORT](https://github.com/OHDSI/CommonDataModel/wiki/COHORT)
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* [COHORT_DEFINITION](https://github.com/OHDSI/CommonDataModel/wiki/COHORT_DEFINITION)
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# SURVEY_CONDUCT
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The SURVEY_CONDUCT table is used to store an instance of a completed survey or questionnaire. It captures details of the individual questionnaire such as who completed it, when it was completed and to which patient treatment or visit it relates to (if any). Each SURVEY has a SURVEY_CONCEPT_ID, a concept in the CONCEPT table identifying the questionnaire e.g. EQ5D, VR12, SF12. Each questionnaire should exist in the CONCEPT table. Each SURVEY can be optionally related to a specific patient visit in order to link it both to the visit during which it was completed and any subsequent visit where treatment was assigned based on the patient's responses.
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Field | Required | Type | Description
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@ -9,8 +7,8 @@ PERSON_ID | Yes | integer | A foreign key identifier to the Person in the PERSON
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SURVEY_CONCEPT_ID | Yes | integer | A foreign key to the predefined Concept identifier in the Standardized Vocabularies reflecting the name and identity of the survey.
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SURVEY_START_DATE | No | date | Date on which the survey was started.
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SURVEY_START_DATETIME | No | datetime | Date and time the survey was started.
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SURVEY_END_DATE | Yes | date | Date on which the survey was completed.
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SURVEY_END_DATETIME | No | datetime | Date and time the survey was completed.
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SURVEY_END_DATE | No | date | Date on which the survey was completed.
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SURVEY_END_DATETIME | Yes | datetime | Date and time the survey was completed.
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PROVIDER_ID | No | integer | A foreign key to the provider in the provider table who was associated with the survey completion.
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ASSISTED_CONCEPT_ID | Yes | integer | A foreign key to the predefined Concept identifier in the Standardized Vocabularies indicating whether the survey was completed with assistance.
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RESPONDENT_TYPE_CONCEPT_ID | Yes | integer | A foreign key to the predefined Concept identifier in the Standardized Vocabularies reflecting the respondent type. Example: Research Associate, Patient.
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@ -14,8 +14,8 @@ Field|Required|Type|Description
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|care_site_id|No|integer|A foreign key to the care site in the care site table that was visited.|
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|visit_source_value|No|varchar(50)|The source code for the visit as it appears in the source data.|
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|visit_source_concept_id|Yes|integer|A foreign key to a Concept that refers to the code used in the source.|
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|admitting_source_concept_id |Yes |integer |A foreign key to the predefined concept in the Place of Service Vocabulary reflecting the admitting source for a visit.|
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|admitting_source_value | No|varchar(50)| The source code for the admitting source as it appears in the source data.|
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|admitted_from_concept_id |Yes |integer |A foreign key to the predefined concept in the Place of Service Vocabulary reflecting where the patient was admitted from.|
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|admitted_from_source_value | No|varchar(50)| The source code for where the patient was admitted from as it appears in the source data.|
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|discharge_to_concept_id |Yes | integer |A foreign key to the predefined concept in the Place of Service Vocabulary reflecting the discharge disposition for a visit.|
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|discharge_to_source_value | No| varchar(50)| The source code for the discharge disposition as it appears in the source data.|
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|preceding_visit_occurrence_id | No |integer|A foreign key to the VISIT_OCCURRENCE table of the visit immediately preceding this visit|
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| 7 | Drug costs are composed of ingredient cost (the amount charged by the wholesale distributor or manufacturer), the dispensing fee (the amount charged by the pharmacy and the sales tax). |
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| 8 | In claims data, generally there is one field representing the total payment from the payer for the service/device/drug. However, this field could be a calculated field if the source data provides separate payment information for the ingredient cost and the dispensing fee in case of prescription benefits. If there is more than one Payer in the source data, several cost records indicate that fact. The Payer reporting this reimbursement should be indicated under the PAYER_PLAN_ID field. |
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| 10 | REVENUE_CODE_CONCEPT_ID: Revenue codes are a method to charge for a class of procedures and conditions in the U.S. hospital system.
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| 11 | DRG_CONCEPT_ID: Diagnosis Related Groups are US codes used to classify hospital cases into one of approximately 500 groups. Only the MS-DRG system should be used (mapped to vocabulary_id 'DRG) and all other DRG values should be mapped to 0 ([THEMIS issue #19](https://github.com/OHDSI/Themis/issues/19)). |
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| 11 | DRG_CONCEPT_ID: Diagnosis Related Groups are US codes used to classify hospital cases into one of approximately 500 groups. APR-DRG codes were recently added to the vocabulary and are now supported along with MS-DRGs ([THEMIS issue #19](https://github.com/OHDSI/Themis/issues/19)). |
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The COST table will store information reporting money or currency amounts. There are three types of cost data, defined in the COST_TYPE_CONCEPT_ID:
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@ -58,15 +58,3 @@ cost_id |person_id| cost_event_id| cost_event_field_concept_id| cost_concept_id|
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|2 |175127601| 1002| *TBD*| 2345| 5032| 0| 44818668| 3 |1/1/2000| |2/28/2000| 0 |0| || 3045|
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|3 |175127601| 1002| *TBD*| 3456| 5032| 0| 44818668| 88 |1/1/2000| | 2/28/2000| 0 |0| || 3045|
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|4 |175127601| 1002| *TBD*| 4567| 5032| 0| 44818668| 113 |1/1/2000| | 2/28/2000| 0 |0| || 3045|
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No.|Convention Description
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:--------|:------------------------------------
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| 1 | The cost information is linked through the COST_EVENT_ID field to its entity, which denotes a record in a table referenced by the COST_EVENT_FIELD_CONCEPT_ID field.
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| 2 | One cost record is generated for each response by a payer. In a claims databases, the payment and payment terms reported by the payer for the goods or services billed will generate one cost record. If the source data has payment information for more than one payer (i.e. primary insurance and secondary insurance payment for one entity), then a cost record is created for each reporting payer. Therefore, it is possible for one procedure to have multiple cost records for each payer, but typically it contains one or no record per entity. Payer reimbursement cost records will be identified by using the PAYER_PLAN_ID field. |
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| 3 | One cost record is generated for each money or currency amount associated with a record in one of the event tables. |
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| 4 | The COST field represents the dollar amount, either incoming or outgoing |
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| 5 | When dealing with summary costs, the cost of the goods or services the provider provides is often not known directly, but derived from the hospital charges multiplied by an average cost-to-charge ratio. This data is currently available for [NIS](https://www.hcup-us.ahrq.gov/db/nation/nis/nisdbdocumentation.jsp) datasets, or any other [HCUP](https://www.hcup-us.ahrq.gov/databases.jsp) datasets. See also cost calculation explanation from AHRQ | 6 | In claims data, total paid is considered the calculated field the payer expects the provider to get reimbursed for goods and services, based on the payer's contractual obligations. |
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| 7 | Drug costs are composed of ingredient cost (the amount charged by the wholesale distributor or manufacturer), the dispensing fee (the amount charged by the pharmacy and the sales tax). |
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| 8 | In claims data, generally there is one field representing the total payment from the payer for the service/device/drug. However, this field could be a calculated field if the source data provides separate payment information for the ingredient cost and the dispensing fee in case of prescription benefits. If there is more than one Payer in the source data, several cost records indicate that fact. The Payer reporting this reimbursement should be indicated under the PAYER_PLAN_ID field. |
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| 10 | REVENUE_CODE_CONCEPT_ID: Revenue codes are a method to charge for a class of procedures and conditions in the U.S. hospital system.
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| 11 | DRG_CONCEPT_ID: Diagnosis Related Groups are US codes used to classify hospital cases into one of approximately 500 groups. Only the MS-DRG system should be used (mapped to vocabulary_id 'DRG) and all other DRG values should be mapped to 0. |
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## LOCATION_HISTORY
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The LOCATION HISTORY table stores relationships between Persons or Care Sites and geographic locations over time.
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Field|Required|Type|Description
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